Svetla Boytcheva Kevin Bretonnel Cohen Guergana Savova Galia Angelova September 2017

Varna, Bulgaria

INCOMA Ltd. 10.26615/978-954-452-044-1_ https://doi.org/10.26615/978-954-452-044-1_ book BioNLP:2017 CureaEric Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 1–7 10.26615/978-954-452-044-1_001 https://doi.org/10.26615/978-954-452-044-1_001 Whenever employed on large datasets, information retrieval works by isolating a subset of documents from the larger dataset and then proceeding with low-level processing of the text. This is usually carried out by means of adding index-terms to each document in the collection. In this paper we deal with automatic document classification and index-term detection applied on large-scale medical corpora. In our methodology we employ a linear classifier and we test our results on the BioASQ training corpora, which is a collection of 12 million MeSH-indexed medical abstracts. We cover both term-indexing, result retrieval and result ranking based on distributed word representations. inproceedings eric:2017:BioNLP MariaMitrofan RaduIon Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 8–14 10.26615/978-954-452-044-1_002 https://doi.org/10.26615/978-954-452-044-1_002 This paper presents the adaptation of the Hidden Markov Models-based TTL part-of-speech tagger to the biomedical domain. TTL is a text processing platform that performs sentence splitting, tokenization, POS tagging, chunking and Named Entity Recognition (NER) for a number of languages, including Romanian. The POS tagging accuracy obtained by the TTL POS tagger exceeds 97\% when TTL's baseline model is updated with training information from a Romanian biomedical corpus. This corpus is developed in the context of the CoRoLa (a reference corpus for the contemporary Romanian language) project. Informative description and statistics of the Romanian biomedical corpus are also provided. inproceedings mitrofan-ion:2017:BioNLP DayneFreitag PaulKalmar EricYeh Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 15–23 10.26615/978-954-452-044-1_003 https://doi.org/10.26615/978-954-452-044-1_003 We consider the problem of populating multi-part knowledge frames from textual information distributed over multiple sentences in a document. We present a corpus constructed by aligning papers from the cellular signaling literature to a collection of approximately 50,000 reference frames curated by hand as part of a decade-long project. We present and evaluate two approaches to the challenging problem of reconstructing these frames, which formalize biological assays described in the literature. One approach is based on classifying candidate records nominated by sentence-local entity co-occurrence. In the second approach, we introduce a novel virtual register machine traverses an article and generates frames, trained on our reference data. Our evaluations show that success in the task ultimately hinges on an integration of evidence spread across the discourse. inproceedings freitag-kalmar-yeh:2017:BioNLP MaximilianZubke Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 24–31 10.26615/978-954-452-044-1_004 https://doi.org/10.26615/978-954-452-044-1_004 The robust extraction of numeric values from clinical narratives is a well known problem in clinical data warehouses. In this paper we describe a dynamic and domain-independent approach to deliver numerical described values from clinical narratives. In contrast to alternative systems, we neither use manual defined rules nor any kind of ontologies or nomenclatures. Instead we propose a topic-based system, that tackles the information extraction as a text classification problem. Hence we use machine learning to identify the crucial context features of a topic-specific numeric value by a given set of example sentences, so that the manual effort reduces to the selection of appropriate sample sentences. We describe context features of a certain numeric value by term frequency vectors which are generated by multiple document segmentation procedures. Due to this simultaneous segmentation approaches, there can be more than one context vector for a numeric value. In those cases, we choose the context vector with the highest classification confidence and suppress the rest. To test our approach, we used a dataset from a german hospital containing 12\,743 narrative reports about laboratory results of Leukemia patients. We used Support Vector Machines (SVM) for classification and achieved an average accuracy of 96\% on a manually labeled subset of 2073 documents, using 10-fold cross validation. This is a significant improvement over an alternative rule based system. inproceedings zubke:2017:BioNLP NataliaGrabar ThierryHamon Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 32–41 10.26615/978-954-452-044-1_005 https://doi.org/10.26615/978-954-452-044-1_005 We assume that unknown words with internal structure (affixed words or compounds) can provide speakers with linguistic cues as for their meaning, and thus help their decoding and understanding. To verify this hypothesis, we propose to work with a set of French medical words. These words are annotated by five annotators. Then, two kinds of analysis are performed: analysis of the evolution of understandable and non-understandable words (globally and according to some suffixes) and analysis of clusters created with unsupervised algorithms on basis of linguistic and extra-linguistic features of the studied words. Our results suggest that, according to linguistic sensitivity of annotators, technical words can be decoded and become understandable. As for the clusters, some of them distinguish between understandable and non-understandable words. Resources built in this work will be made freely available for the research purposes. inproceedings grabar-hamon:2017:BioNLP Seid MuhieYimam SteffenRemus AlexanderPanchenko AndreasHolzinger ChrisBiemann Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 42–48 10.26615/978-954-452-044-1_006 https://doi.org/10.26615/978-954-452-044-1_006 In this paper, we describe the concept of entity-centric information access for the biomedical domain. With entity recognition technologies approaching acceptable levels of accuracy, we put forward a paradigm of document browsing and searching where the entities of the domain and their relations are explicitly modeled to provide users the possibility of collecting exhaustive information on relations of interest. We describe three working prototypes along these lines: NEW/S/LEAK, which was developed for investigative journalists who need a quick overview of large leaked document collections; STORYFINDER, which is a personalized organizer for information found in web pages that allows adding entities as well as relations, and is capable of personalized information management; and adaptive annotation capabilities of WEBANNO, which is a general-purpose linguistic annotation tool. We will discuss future steps towards the adaptation of these tools to biomedical data, which is subject to a recently started project on biomedical knowledge acquisition. A key difference to other approaches is the centering around the user in a Human-in-the-Loop machine learning approach, where users define and extend categories and enable the system to improve via feedback and interaction. inproceedings yimam-EtAl:2017:BioNLP VictorBellon RaulRodriguez-Esteban Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 49–54 10.26615/978-954-452-044-1_007 https://doi.org/10.26615/978-954-452-044-1_007 We explored a new approach to named entity recognition based on hundreds of machine learning models, each trained to distinguish a single entity, and showed its application to gene name identification (GNI). The rationale for our approach, which we named “one model per entity” (OMPE), was that increasing the number of models would make the learning task easier for each individual model. Our training strategy leveraged freely-available database annotations instead of manually-annotated corpora. While its performance in our proof-of-concept was disappointing, we believe that there is enough room for improvement that such approaches could reach competitive performance while eliminating the cost of creating costly training corpora. inproceedings bellon-rodriguezesteban:2017:BioNLP CamiloThorne RomanKlinger Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 55–63 10.26615/978-954-452-044-1_008 https://doi.org/10.26615/978-954-452-044-1_008 Systems which build on top of information extraction are typically challenged to extract knowledge that, while correct, is not yet well-known. We hypothesize that a good confidence measure for relational information has the property that such interesting information is found between information extracted with very high confidence and very low confidence. We discuss confidence estimation for the domain of biomedical protein-protein relation discovery in biomedical literature. As facts reported in papers take some time to be validated and recorded in biomedical databases, such task gives rise to large quantities of unknown but potentially true candidate relations. It is thus important to rank them based on supporting evidence rather than discard them. In this paper, we discuss this task and propose different approaches for confidence estimation and a pipeline to evaluate such methods. We show that the most straight-forward approach, a combination of different confidence measures from pipeline modules seems not to work well. We discuss this negative result and pinpoint potential future research directions. inproceedings thorne-klinger:2017:BioNLP SvetlaBoytcheva IvelinaNikolova GaliaAngelova ZhivkoAngelov Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 64–72 10.26615/978-954-452-044-1_009 https://doi.org/10.26615/978-954-452-044-1_009 We describe a method which extracts Association Rules from texts in order to recognise verbalisations of risk factors. Usually some basic vocabulary about risk factors is known but medical conditions are expressed in clinical narratives with much higher variety. We propose an approach for data-driven learning of specialised medical vocabulary which, once collected, enables early alerting of potentially affected patients. The method is illustrated by experimens with clinical records of patients with Chronic Obstructive Pulmonary Disease (COPD) and comorbidity of CORD, Diabetes Melitus and Schizophrenia. Our input data come from the Bulgarian Diabetic Register, which is built using a pseudonymised collection of outpatient records for about 500,000 diabetic patients. The generated Association Rules for CORD are analysed in the context of demographic, gender, and age information. Valuable anounts of meaningful words, signalling risk factors, are discovered with high precision and confidence. inproceedings boytcheva-EtAl:2017:BioNLP1 ThierryHamon VincentTabanou FleurMougin NataliaGrabar FrantzThiessard Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 73–80 10.26615/978-954-452-044-1_010 https://doi.org/10.26615/978-954-452-044-1_010 When patients take more than one medication, they may be at risk of drug interactions, which means that a given drug can cause unexpected effects when taken in combination with other drugs. Similar effects may occur when drugs are taken together with some food or beverages. For instance, grapefruit has interactions with several drugs, because its active ingredients inhibit enzymes involved in the drugs metabolism and can then cause an excessive dosage of these drugs. Yet, information on food/drug interactions is poorly researched. The current research is mainly provided by the medical domain and a very tentative work is provided by computer sciences and NLP domains. One factor that motivates the research is related to the availability of the annotated corpora and the reference data. The purpose of our work is to describe the rationale and approach for creation and annotation of scientific corpus with information on food/drug interactions. This corpus contains 639 MEDLINE citations (titles and abstracts), corresponding to 5,752 sentences. It is manually annotated by two experts. The corpus is named POMELO. This annotated corpus will be made available for the research purposes. inproceedings hamon-EtAl:2017:BioNLP IvajloRadev KirilSimov GaliaAngelova SvetlaBoytcheva Proceedings of the Biomedical NLP Workshop associated with RANLP 2017 September 2017

Varna, Bulgaria

INCOMA Ltd. 81–87 10.26615/978-954-452-044-1_011 https://doi.org/10.26615/978-954-452-044-1_011 In this paper we describe annotation process of clinical texts with morphosyntactic and semantic information. The corpus contains 1,300 discharge letters in Bulgarian language for patients with Endocrinology and Metabolic disorders. The annotated corpus will be used as a Gold standard for information extraction evaluation of test corpus of 6,200 discharge letters. The annotation is performed within Clark system –- an XML Based System For Corpora Development. It provides mechanism for semi-automatic annotation first running a pipeline for Bulgarian morphosyntactic annotation and a cascaded regular grammar for semantic annotation is run, then rules for cleaning of frequent errors are applied. At the end the result is manually checked. At the end we hope also to be able to adapted the morphosyntactic tagger to the domain of clinical narratives as well. inproceedings boytcheva-EtAl:2017:BioNLP2